Special purpose UI prototyping tools, like the ones listed on C2 Wiki, offer a convenient blend of usability and flexibility. I have tried some of these tools. I was looking for something that -
doesn’t become unwieldy when used to prototype a large and complex GUI
allows me to use my own screenshots/images/icons
allows me to modify the prototype without making it a hair-pulling experience.
can prototype all aspects and artifacts of modern web and desktop interfaces, specially -
tree controls - you will be surprised how many prototyping tools don’t have this. Pencil, I am looking at you :) tabbed panels - can you position your tabs at the bottom ? on the right edge ? film strips ribbons NavBars ...